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Yorodumi- PDB-5byl: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5byl | ||||||
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| Title | Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPCP and Magnesium | ||||||
Components | Bifunctional AAC/APH | ||||||
Keywords | TRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance | ||||||
| Function / homology | Function and homology informationaminoglycoside 2''-phosphotransferase / aminoglycoside phosphotransferase activity / N-acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ATP binding / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Caldwell, S.J. / Berghuis, A.M. | ||||||
| Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2016Title: Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia. Authors: Caldwell, S.J. / Huang, Y. / Berghuis, A.M. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5byl.cif.gz | 538.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5byl.ent.gz | 442.8 KB | Display | PDB format |
| PDBx/mmJSON format | 5byl.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5byl ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byl | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 5iqaC ![]() 5iqbC ![]() 5iqcC ![]() 5iqdC ![]() 5iqeC ![]() 5iqfC ![]() 5iqgC ![]() 5iqhC ![]() 5iqiC C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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| Details | SAXS |
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Components
-Protein , 1 types, 4 molecules ABCD
| #1: Protein | Mass: 35948.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) Source method: isolated from a genetically manipulated source Details: C-terminal domain of AAC(6')-Ie/APH(2'')-Ia bifunctional enzyme, residues 175-479 Source: (gene. exp.) ![]() ![]() References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 5 types, 1081 molecules 








| #2: Chemical | ChemComp-GCP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
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| Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 80-120mM MgCl2, 8% Glycerol, 10% PEG3350, 100mM HEPES pH 7.5 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
| Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 26, 2013 |
| Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
| Reflection | Resolution: 2.15→58.92 Å / Num. obs: 82837 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Net I/av σ(I): 3.8 / Net I/σ(I): 12.3 |
| Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.6 / % possible all: 65.6 |
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Processing
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| Refinement | Method to determine structure: FOURIER SYNTHESISStarting model: APH(2'')-Ia GMPPNP-Mg complex Resolution: 2.15→58.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Authors state that MG 700 and GCP 500 of chain C have a clash that appears to be a consequence of multiple discrete states in the active site. Refinement of multiple occupancy MG 700 ...Details: Authors state that MG 700 and GCP 500 of chain C have a clash that appears to be a consequence of multiple discrete states in the active site. Refinement of multiple occupancy MG 700 diverged from physiologically sensible positions, and so the single occupancy was retained, despite this clash.
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 47.77 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.15→58.92 Å
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| Refine LS restraints |
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X-RAY DIFFRACTION
Canada, 1items
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